How do I stop STAR from generating a new reference each time the workflow is run on a sample?
Everytime I run gatk4-rnaseq-germline-snps-indels for each sample, the STAR reference step is created again. I believe this is the case because each run is an independent cromwell-execution. Is there something I'm missing or should I "adapt" the workflow to check for the file and re-use if already present?
This is the source for the aforementioned issue:
Another question, for some files in the output (inside cromwell-executions), the owner is me who ran the workflow, and for some is the root (which docker runs as). However, I don't have root access on this particular server, I'm only a user belonging to the docker group. Then, how can I access these files or change their permission? Is this possible?
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